mf6adj 1.0.0__tar.gz

mf6adj-1.0.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
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+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
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+docs/source/examples/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
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+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
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+# MacOS files
+.DS_Store
+
+# Examples result directories
+examples/ex-gwf-zaidel/
+examples/freyberg/
+examples/sanpedro/
+examples/xd_box_chd_ana_working
+examples/synthdewater_working
+autotest/*_test*/
+.figures/
+
+.temp/

mf6adj-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mf6adj
+Version: 1.0.0
+Summary: mf6adj is a Python package for adjoint-state sensitivity analysis with MODFLOW 6
+Project-URL: Documentation, https://mf6adj.readthedocs.io
+Project-URL: Bug Tracker, https://github.com/INTERA-Inc/mf6adj/issues
+Project-URL: Source Code, https://github.com/INTERA-Inc/mf6adj
+Author: INTERA Incorporated
+Maintainer: INTERA Incorporated
+License: CC0-1.0
+Keywords: MODFLOW,adjoint,groundwater,hydrogeology
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Hydrology
+Requires-Python: >=3.10
+Requires-Dist: flopy>=3.10.0
+Requires-Dist: geopandas>=1.0.0
+Requires-Dist: h5py>=3.0.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: modflowapi>=0.2.0
+Requires-Dist: numpy>=2.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pyemu>=1.4.0
+Requires-Dist: scipy>=1.7.0
+Provides-Extra: dev
+Requires-Dist: boltons; extra == 'dev'
+Requires-Dist: codespell[toml]>=2.2.2; extra == 'dev'
+Requires-Dist: filelock; extra == 'dev'
+Requires-Dist: flaky; extra == 'dev'
+Requires-Dist: ipykernel; extra == 'dev'
+Requires-Dist: jupyter; extra == 'dev'
+Requires-Dist: jupyter-client>=8.4.0; extra == 'dev'
+Requires-Dist: modflow-devtools>=1.9.1; extra == 'dev'
+Requires-Dist: myst-parser; extra == 'dev'
+Requires-Dist: nbconvert; extra == 'dev'
+Requires-Dist: nbmake; extra == 'dev'
+Requires-Dist: nbsphinx; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest-dotenv; extra == 'dev'
+Requires-Dist: pytest-order; extra == 'dev'
+Requires-Dist: pytest-xdist; extra == 'dev'
+Requires-Dist: pytest>=9.0.2; extra == 'dev'
+Requires-Dist: pyyaml; extra == 'dev'
+Requires-Dist: rtds-action; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: shapely; extra == 'dev'
+Requires-Dist: sphinx-rtd-theme>=1; extra == 'dev'
+Requires-Dist: sphinx>=7.1.2; extra == 'dev'
+Requires-Dist: tomli-w; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: boltons; extra == 'doc'
+Requires-Dist: codespell[toml]>=2.2.2; extra == 'doc'
+Requires-Dist: filelock; extra == 'doc'
+Requires-Dist: flaky; extra == 'doc'
+Requires-Dist: ipykernel; extra == 'doc'
+Requires-Dist: jupyter; extra == 'doc'
+Requires-Dist: jupyter-client>=8.4.0; extra == 'doc'
+Requires-Dist: modflow-devtools>=1.9.1; extra == 'doc'
+Requires-Dist: myst-parser; extra == 'doc'
+Requires-Dist: nbconvert; extra == 'doc'
+Requires-Dist: nbmake; extra == 'doc'
+Requires-Dist: nbsphinx; extra == 'doc'
+Requires-Dist: pytest-cov; extra == 'doc'
+Requires-Dist: pytest-dotenv; extra == 'doc'
+Requires-Dist: pytest-order; extra == 'doc'
+Requires-Dist: pytest-xdist; extra == 'doc'
+Requires-Dist: pytest>=9.0.2; extra == 'doc'
+Requires-Dist: pyyaml; extra == 'doc'
+Requires-Dist: rtds-action; extra == 'doc'
+Requires-Dist: ruff; extra == 'doc'
+Requires-Dist: shapely; extra == 'doc'
+Requires-Dist: sphinx-rtd-theme>=1; extra == 'doc'
+Requires-Dist: sphinx>=7.1.2; extra == 'doc'
+Requires-Dist: tomli-w; extra == 'doc'
+Provides-Extra: lint
+Requires-Dist: codespell[toml]>=2.2.2; extra == 'lint'
+Requires-Dist: ruff; extra == 'lint'
+Provides-Extra: test
+Requires-Dist: boltons; extra == 'test'
+Requires-Dist: codespell[toml]>=2.2.2; extra == 'test'
+Requires-Dist: filelock; extra == 'test'
+Requires-Dist: flaky; extra == 'test'
+Requires-Dist: ipykernel; extra == 'test'
+Requires-Dist: jupyter; extra == 'test'
+Requires-Dist: jupyter-client>=8.4.0; extra == 'test'
+Requires-Dist: modflow-devtools>=1.9.1; extra == 'test'
+Requires-Dist: nbmake; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-dotenv; extra == 'test'
+Requires-Dist: pytest-order; extra == 'test'
+Requires-Dist: pytest-xdist; extra == 'test'
+Requires-Dist: pytest>=9.0.2; extra == 'test'
+Requires-Dist: ruff; extra == 'test'
+Requires-Dist: shapely; extra == 'test'
+Requires-Dist: tomli-w; extra == 'test'
+Description-Content-Type: text/markdown
+
+# mf6adj
+
+![mf6adj](https://raw.githubusercontent.com/INTERA-Inc/mf6adj/master/.images/mf6adj.png)
+
+**mf6adj** is a Python package for adjoint-state sensitivity analysis with
+MODFLOW 6.  It uses the [MODFLOW 6 API](https://github.com/MODFLOW-USGS/modflowapi)
+to access the internal solution components at run time — no modifications to
+MODFLOW 6 are required.  Given one or more user-defined performance measures
+(heads, boundary fluxes, or composite objectives), mf6adj computes the
+sensitivity of each measure to model parameters across the full model domain.
+
+## Installation
+
+**pip**
+
+```bash
+pip install mf6adj
+```
+
+**conda-forge**
+
+```bash
+conda install -c conda-forge mf6adj
+```
+
+mf6adj drives MODFLOW 6 through its shared library (`libmf6`).  The easiest
+way to get both is through the
+[`flopy`](https://github.com/modflowpy/flopy) helper:
+
+```bash
+get-modflow --subset mf6,libmf6 :python
+```
+
+## Quick start
+
+```python
+import flopy
+import mf6adj
+
+# locate the MF6 binary and shared library in the active conda environment
+mf6_bin, lib_name = mf6adj.get_conda_mf6_paths()
+
+# run the baseline forward model
+flopy.run_model(exe_name=mf6_bin, namefile=None, model_ws="path/to/model")
+
+# write a performance-measure file
+with open("path/to/model/model.adj", "w") as f:
+    f.write("begin performance_measure head_obs\n")
+    f.write("1 1 1 5 5 head direct 1.0 -1.0e+30\n")
+    f.write("end performance_measure\n")
+
+# solve forward and adjoint
+adj = mf6adj.Mf6Adj("model.adj", str(lib_name), working_directory="path/to/model")
+adj.solve_forward_model()
+sensitivity_dfs = adj.solve_adjoint()
+adj.finalize()
+
+print(sensitivity_dfs["head_obs"])
+```
+
+## Documentation
+
+Full documentation, including API reference and example notebooks, is available
+at [mf6adj.readthedocs.io](https://md6adj.readthedocs.io).
+
+## How to cite
+
+If you use mf6adj in your work, please cite:
+
+> Hayek, M., White, J. T., Markovich, K. H., Hughes, J. D., & Lavenue, M. (2025).
+> MF6-ADJ: A Non-Intrusive Adjoint Sensitivity Capability for MODFLOW 6.
+> *Groundwater*, 63(6), 874–888. https://doi.org/10.1111/gwat.70025
+
+## License
+
+[CC0 1.0 Universal](https://creativecommons.org/publicdomain/zero/1.0/)

mf6adj-1.0.0/README.md

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+# mf6adj
+
+![mf6adj](https://raw.githubusercontent.com/INTERA-Inc/mf6adj/master/.images/mf6adj.png)
+
+**mf6adj** is a Python package for adjoint-state sensitivity analysis with
+MODFLOW 6.  It uses the [MODFLOW 6 API](https://github.com/MODFLOW-USGS/modflowapi)
+to access the internal solution components at run time — no modifications to
+MODFLOW 6 are required.  Given one or more user-defined performance measures
+(heads, boundary fluxes, or composite objectives), mf6adj computes the
+sensitivity of each measure to model parameters across the full model domain.
+
+## Installation
+
+**pip**
+
+```bash
+pip install mf6adj
+```
+
+**conda-forge**
+
+```bash
+conda install -c conda-forge mf6adj
+```
+
+mf6adj drives MODFLOW 6 through its shared library (`libmf6`).  The easiest
+way to get both is through the
+[`flopy`](https://github.com/modflowpy/flopy) helper:
+
+```bash
+get-modflow --subset mf6,libmf6 :python
+```
+
+## Quick start
+
+```python
+import flopy
+import mf6adj
+
+# locate the MF6 binary and shared library in the active conda environment
+mf6_bin, lib_name = mf6adj.get_conda_mf6_paths()
+
+# run the baseline forward model
+flopy.run_model(exe_name=mf6_bin, namefile=None, model_ws="path/to/model")
+
+# write a performance-measure file
+with open("path/to/model/model.adj", "w") as f:
+    f.write("begin performance_measure head_obs\n")
+    f.write("1 1 1 5 5 head direct 1.0 -1.0e+30\n")
+    f.write("end performance_measure\n")
+
+# solve forward and adjoint
+adj = mf6adj.Mf6Adj("model.adj", str(lib_name), working_directory="path/to/model")
+adj.solve_forward_model()
+sensitivity_dfs = adj.solve_adjoint()
+adj.finalize()
+
+print(sensitivity_dfs["head_obs"])
+```
+
+## Documentation
+
+Full documentation, including API reference and example notebooks, is available
+at [mf6adj.readthedocs.io](https://md6adj.readthedocs.io).
+
+## How to cite
+
+If you use mf6adj in your work, please cite:
+
+> Hayek, M., White, J. T., Markovich, K. H., Hughes, J. D., & Lavenue, M. (2025).
+> MF6-ADJ: A Non-Intrusive Adjoint Sensitivity Capability for MODFLOW 6.
+> *Groundwater*, 63(6), 874–888. https://doi.org/10.1111/gwat.70025
+
+## License
+
+[CC0 1.0 Universal](https://creativecommons.org/publicdomain/zero/1.0/)

mf6adj-1.0.0/examples/clear_output_all.py

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+import os
+import pathlib as pl
+
+
+def find_files_with_extension(directory, extension):
+    """
+    Finds all files with the specified extension in the given directory and
+    its subdirectories.
+
+    Args:
+        directory: The path to the directory to search.
+        extension: The file extension to search for (e.g., ".txt", ".pdf").
+
+    Returns:
+        A list of Path objects representing the files found.
+    """
+    path = pl.Path(directory)
+    if not path.is_dir():
+        raise NotADirectoryError(f"'{directory}' is not a valid directory.")
+
+    return list(path.rglob(f"*{extension}"))
+
+
+directory_path = ".."
+file_extension = ".ipynb"
+exclude_paths = (
+    ".ipynb_checkpoints",
+    "site-packages",
+    ".temp",
+)
+notebook_count = 0
+try:
+    files = find_files_with_extension(directory_path, file_extension)
+    if files:
+        print(f"Files with extension '{file_extension}' found in '{directory_path}':")
+        for file in files:
+            exclude = False
+            for epath in exclude_paths:
+                if epath in str(file):
+                    exclude = True
+                    break
+            if exclude:
+                print(f"skipping...{file}")
+            else:
+                print(f"clearing...{file}")
+                os.system(
+                    "jupyter nbconvert --ClearOutputPreprocessor.enabled=True "
+                    + f"--ClearMetadataPreprocessor.enabled=True --inplace {file}"
+                )
+                notebook_count += 1
+    else:
+        print(
+            f"No files with extension '{file_extension}' found in '{directory_path}'."
+        )
+    print(f"notebooks cleared...{notebook_count}")
+
+except NotADirectoryError as e:
+    print(e)